hdallatorre commited on
Commit
d6aeb72
1 Parent(s): 1eb5300

Update README.md

Browse files
Files changed (1) hide show
  1. README.md +28 -9
README.md CHANGED
@@ -5,7 +5,9 @@
5
  ---
6
 
7
  # Dataset Card for Dataset Name
8
- The nucleotide_transformer_downstream_tasks_public dataset features 2 of the 18 downstream tasks classification downstream tasks presented in the Nucleotide Transformer paper.
 
 
9
  ## Dataset Description
10
 
11
  - **Repository:** [Nucleotide Transformer](https://github.com/instadeepai/nucleotide-transformer)
@@ -13,18 +15,35 @@ The nucleotide_transformer_downstream_tasks_public dataset features 2 of the 18
13
 
14
  ### Dataset Summary
15
 
16
- This dataset features two classification datasets that were introduced in two different genomics papers:
17
- - [DeePromoter: Robust Promoter Predictor Using Deep Learning](https://www.frontiersin.org/articles/10.3389/fgene.2019.00286/full): The datasets features 3,065 TATA promoters and 26,532 non-TATA promoters, with each promoter yielding a negative sequence by randomly sampling parts of the sequence.
18
  - [A deep learning framework for enhancer prediction using word embedding and sequence generation](https://www.sciencedirect.com/science/article/abs/pii/S0301462222000643): To build the training dataset, the authors collect 742 strong
19
- enhancers, 742 weak enhancers and 1484 non-enhancers, and augment the dataset with 6000 synthetic enhancers and 6000 synthetic non-enhancers produced with a generative model. The test dataset is comprised of 100 strong enhancers, 100 weak enhancers and 200 non enhancers. The original paper also uses this dataset to do both binary classification (i.e a sample gets classified as non-enhancer or enhancer) and 3-class classification (i.e a sample gets classified as non-enhancer, weak enhancer or strong enhancer). Here the dataset has been processed to do binary classification only.
 
 
20
 
21
  ## Dataset Structure
22
-
23
  ```
24
- | Task | Number of train sequences | Number of test sequences |
25
- | ------------- | --------------------------| --------------------------|
26
- | promoter_all | 53,276 | 5,920 |
27
- | enhancers | 14,968 | 400 |
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
28
  ```
29
 
30
 
 
5
  ---
6
 
7
  # Dataset Card for Dataset Name
8
+ The `nucleotide_transformer_downstream_tasks` dataset features the 18 downstream tasks presented in the Nucleotide Transformer paper. They consist of both binary and multi-class classification tasks that aim at providing a consistent genomics benchmark.
9
+
10
+
11
  ## Dataset Description
12
 
13
  - **Repository:** [Nucleotide Transformer](https://github.com/instadeepai/nucleotide-transformer)
 
15
 
16
  ### Dataset Summary
17
 
18
+ The different datasets are collected from 4 different genomics papers:
19
+ - [DeePromoter: Robust Promoter Predictor Using Deep Learning](https://www.frontiersin.org/articles/10.3389/fgene.2019.00286/full): The datasets features 3,065 TATA promoters and 26,532 non-TATA promoters, with each promoter yielding a negative sequence by randomly sampling parts of the sequence. The `promoter_all` dataset will feature all the promoters and their negative counterparts, while the `promoter_tata` and `promoter_no_tata` respectively provide the TATA and non-TATA parts of the dataset.
20
  - [A deep learning framework for enhancer prediction using word embedding and sequence generation](https://www.sciencedirect.com/science/article/abs/pii/S0301462222000643): To build the training dataset, the authors collect 742 strong
21
+ enhancers, 742 weak enhancers and 1484 non-enhancers, and augment the dataset with 6000 synthetic enhancers and 6000 synthetic non-enhancers produced with a generative model. The test dataset is comprised of 100 strong enhancers, 100 weak enhancers and 200 non enhancers. The original paper uses this dataset to do both binary classification (i.e a sample gets classified as non-enhancer or enhancer) and 3-class classification (i.e a sample gets classified as non-enhancer, weak enhancer or strong enhancer). Both tasks are respectively tackled in the `enhancers` and `enhancers_types` datasets.
22
+ - [SpliceFinder: ab initio prediction of splice sites using convolutional neural network](https://pubmed.ncbi.nlm.nih.gov/31881982): The authors introduce a dataset containing 10,000 samples of donor site, acceptor site, and non-splice-site, resulting in 30,000 total samples that are featured in the `splice_sites_all` dataset. The datasets `splice_sites_acceptors` and `splice_sites_donors` are the same dataset where the donors and acceptors splice sites have been removed respectively.
23
+ - [Qualitatively predicting acetylation and methylation areas in DNA sequences](https://pubmed.ncbi.nlm.nih.gov/16901084/): The paper introduces a set of datasets featuring epigenetic marks identified in the yeast genome, namely acetylation and metylation nucleosome occupancies. Nucleosome occupancy values in these ten datasets were obtained with Chip-Chip experiments and further processed into positive and negative observations to provide the datasets corresponding to the following histone marks: `H3`, `H4`, `H3K9ac`, `H3K14ac`, `H4ac`, `H3K4me1`, `H3K4me2`, `H3K4me3`, `H3K36me3` and `H3K79me3`
24
 
25
  ## Dataset Structure
 
26
  ```
27
+ | Task | Number of train sequences | Number of test sequences | Number of labels |
28
+ | --------------------- | ------------------------- | ------------------------ | ---------------- |
29
+ | promoter_all | 53,276 | 5,920 | 2 |
30
+ | promoter_tata | 5,509 | 621 | 2 |
31
+ | promoter_no_tata | 47,767 | 5,299 | 2 |
32
+ | enhancers | 14,968 | 400 | 2 |
33
+ | enhancers_types | 14,968 | 400 | 3 |
34
+ | splice_sites_all | 27,000 | 3,000 | 3 |
35
+ | splice_sites_acceptor | 19,961 | 2,218 | 2 |
36
+ | splice_sites_donor | 19,775 | 2,198 | 2 |
37
+ | H3 | 13,468 | 1,497 | 2 |
38
+ | H4 | 13,140 | 1,461 | 2 |
39
+ | H3K9ac | 25,003 | 2,779 | 2 |
40
+ | H3K14ac | 29,743 | 3,305 | 2 |
41
+ | H4ac | 30,685 | 3,410 | 2 |
42
+ | H3K4me1 | 28,509 | 3,168 | 2 |
43
+ | H3K4me2 | 27,614 | 3,069 | 2 |
44
+ | H3K4me3 | 33,119 | 3,680 | 2 |
45
+ | H3K36me3 | 31,392 | 3,488 | 2 |
46
+ | H3K79me3 | 25,953 | 2,884 | 2 |
47
  ```
48
 
49